Time (x-axis) vs performance parameters (y-axis) (CPU utilized in the top panel and cache memory in the bottom panel) during TopHat run for single end reads (SRR094775). The standalone system has 16 GB of onboard RAM and 8 cores (3.3 GHz) CPU. Black box indicates the region where CPU is underutilized. Numbers in bold below the arrows indicate the time span of execution of different steps of TopHat: 1: filter_reads. 2: gene_align. 3: genome_align. 4: find_juncs. 5: junc_align. 6: span_reads. 7: report.